Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 1315 |
| PDBID: | 5F7L |
| Chains: | B_A |
| Organism: | Helicobacter pylori, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.74 |
| Reference: | 10.1016/j.chom.2015.12.004 |
| Antibody | |
| Antibody: | Nb-ER14 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Blood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >5F7L_B|Chain B, D|Nanobody Nb-ER14|Lama glama (9844) QVQLQESGGGLVQPGGSLRLSCAASGSIYSLIAMGWYRQAPGKEHELVATISSGSTTYYADSVKGRFTISRDNAKNTLYLQMNSLKPEDTAMYYCAAYSDRLTDCSNCEADYWGQGTQVTVSHHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >5F7L_A|Chain A, C|Adhesin binding fucosylated histo-blood group antigen|Helicobacter pylori (210) ASWSHPQFEKSGGGGGLVPRGSGIQDLSDNYENLSKLLTRYSTLNTLIKLSADPSAINAARENLGASAKNLIGDTKNSPAYQAVLLAINAAVGFWNVLGYATQCGGNANGQESTSSTTIFNNEPGYRSTSITCSLNRYKPGYYGPMSIENFKKLNEAYQILQTALNKGLPALKENNGTVSVTYTYTCSGEGNDNCSKKATGVSDQNGGTKTKTQTIDGKTVTTTISSKVVDSQAKGNTTRVSYTEITNKLDGVPDSAQALLAQASTLINTINTACPYFSVTNKSGGPQMEPTRGKLCGFTEEISAIQKMITDAQELVNQTSVINEHEQSTPVGGNNGKPFNPFTDASFAQGMLANASAQAKMLNLAHQVGQTINPDNLTGTFKNFVTGFLATCNNKSTAGTSGTQGSPPGTVTTQTFASGCAYVEQTITNLNNSIAHFGTQEQQIQQAENIADTLVNFGSHHHHHH |
Interaction
1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å2 were classified as interacting residues.
Interacting residues (ΔSASA based)
| Chain residues position delta_SASA
: residuesposition B: GLN1 VAL2 GLN3 GLN5 SER7 GLY26 SER27 ILE28 TYR29 SER30 HIS45 SER99 ASP100 ARG101 LEU102 THR103 ASP104 CYS108 GLU109 ALA110 ASP111 TYR112 TRP113 GLY114 GLN115 A: TYR102 ALA103 THR104 GLN105 CYS106 THR116 SER117 THR119 ILE121 TYR128 THR134 SER136 LEU137 ASN138 ARG139 TYR140 TYR145 GLY146 PRO147 SER190 GLY191 GLU192 THR241 ARG242 VAL243 TYR279 SER281 VAL282 THR283 ARG295 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
